Medical Microbiology I - Lecture5

Medical Microbiology I

Lecture 5Lecture 5

Evolution of Bacterial Taxonomy

Taxonomy

Taxonomy

TAXONOMY - hierarchical system for classifying and identifying organisms (the science of classification of living organisms)

Developed by Swedish scientist Carolus Developed by Swedish scientist Carolus Linnaeus in the 18th century - book Systema naturae (translates as System of Nature) -meaning a classification of all known natural life

Each species is assigned a two-part LATINISEDname, or BINOMIAL

Taxonomy

Linnaeus's taxonomy system has TWO main features that contribute to its ease of use in naming and grouping organisms.

1. The FIRST is the use of binomial nomenclature.1. The FIRST is the use of binomial nomenclature.

An organism's scientific name is comprised of a combination of two terms.

These terms are the genus name and the species epithet.

Both of these terms are ITALICISED and the genus name is also CAPITALISED.

Taxonomy

E.g., the scientific name for human is Homo

sapiens - meaning wise man

The genus name is Homo and the species is

sapiens. sapiens.

These terms are unique and no other species

can have this same name.

Taxonomy

e.g. Escherichia coli - Escherichia is the genus

name and coli is the species epithet

Sometimes the genus is designated by a single

letter abbreviation e.g. E. coliletter abbreviation e.g. E. coli

The abbreviation sp. is used to designate a

single species, whereas the abbreviation spp.

is used to designate more than one species

Taxonomy

2. The SECOND feature of Linnaeus's

taxonomy system that simplifies organism

classification is the ordering of species into

broad categories. broad categories.

There are seven major categories: Kingdom,

Phylum, Class, Order, Family, Genus, and

Species.

Taxonomy

Taxonomy

A good aid for remembering

these categories is the

mnemonic device:

Keep Plates Clean Or Family

Gets Sick

Taxonomy

Some of these categories can be further

divided into intermediate categories such as

subphyla, suborders, superfamilies, and

superclasses. superclasses.

An example of this taxonomy scheme is:

Taxonomy

Kingdom

Phylum

Subphylum

Superclass

Class

Family

Subfamily

Genus

Subgenus

Species Class

Subclass

Superorder

Order

Suborder

Superfamily

Species

Subspecies

Taxonomy

Classification

Brown bear House cat Dog Killer whale Wolf

Kingdom Animalia Animalia Animalia Animalia Animalia

Phylum Chordata Chordata Chordata Chordata Chordata

Class Mammalia Mammalia Mammalia Mammalia Mammalia

Order Carnivora Carnivora Carnivora Cetacea Carnivora

Family Ursidae Felidae Canidae Delphinidae Canidae

Genus Ursus Felis Canis Orcinus Canis

Species Ursus arctos Felis catus Canis familiaris Orcinus orca Canis lupus

Taxonomy

The first step of hierarchical classification is

built into the binomial for a species

Species that are closely related are grouped

into the same genus (plural: genera)into the same genus (plural: genera)

Beyond the grouping of species within genera,

taxonomy extends to progressively broader

categories of classification

Taxonomy

It places related genera in the same family,

puts families into orders, orders into classes,

classes into phyla (singular: phylum), phyla

into kingdoms, and kingdoms into domainsinto kingdoms, and kingdoms into domains

Each taxonomic level is more comprehensive

than the previous one

The named taxonomic unit at any level is

called a taxon (plural: taxa)

Taxonomy

Only the genus name and specific epithet are

italicised, and all taxa at the genus level and

beyond are capitalised

Major Lineages of Life

Previously, there were only two kingdom: Animalia and Plantae (according to Linnaeus)

Even with the discovery of the diverse microbial world, the two-kingdom system microbial world, the two-kingdom system persisted

Bacteria were placed in the plant kingdom using their rigid cell wall as a justification

Eukaryotic unicellular organisms with chloroplasts were also considered plants


Fungi were classified under plant kingdom partly because they are sedentary, even though fungi are not photosynthetic and have little in common structurally with green plants

In the two-kingdom system, unicellular creatures that move and ingest food e.g.protozoa were called animals

Microbes such as Euglena that move but are photosynthetic were placed in both the animal and plant kingdom by the different researchers


Robert H. Whittaker, of Cornell University

introduced the five-kingdom system in 1969 -

Monera, Protista, Plantae, Fungi, and Animalia

The five-kingdom system recognises the two The five-kingdom system recognises the two

fundamentally different types of cell types,

prokaryotic and eukaryotic

It sets the prokaryotes apart from all

eukaryotes by placing them in their own

kingdom, Monera


Whittaker distinguished 3 kingdoms of multicellular eukaryotes partly on their nutrition - Plantae, Fungi, and Animalia

Plants are autotrophic in nutritional mode, making their food by photosynthesismaking their food by photosynthesis

Fungi are heterotrophic organisms that are absorptive in nutritional mode

Most fungi are decomposers that live embedded in their food source, secreting digestive enzymes and absorbing the small organic molecules that are the products of digestion


Most animals live by ingesting food and

digesting it within specialised cavities

In Whittakers five-kingdom system, Protista

consisted of all eukaryotes that did not fit the consisted of all eukaryotes that did not fit the

definition of plants, fungi, or animals

Most protists are unicellular forms

The five-kingdom system was used in biology

for over 20 years


In the late 1970s, Carl R. Woese devised a new system on evidences that there are 2 distinct lineages of prokaryotes based on molecular data (differences in their rRNA sequences)

These new data led to a three-domain system

The three domains - Bacteria, Archaea, and Eukaryota (Eukarya), are essentially superkingdoms, a taxonomic level even higher than the kingdom level


Woese considered other conserved molecules in cells including certain proteins, and conserved genes (DNA), but settled for the ssrRNA for a number of reasons.

1. rRNA is found in all cells.

2. rRNA is present in thousands of copies and is easy to isolate from cells

3. rRNA can be analyzed to determine the exact sequence of nucleotide bases in its makeup.


4. The sequence of bases in RNA is a

complementary COPY of the sequence of

bases in the gene (DNA) that encodes for

RNA.RNA.

5. Base sequences in different rRNA molecules

can be compared by computer analyses and

statistical methods to reveal precise

similarities and differences in cellular

genomes.


In this three-domain system, there are two

domains of prokaryotes (Archaea and

Bacteria) and one domain (Eukarya), which

includes all eukaryotic organismsincludes all eukaryotic organisms

Archaea comes from the word archae,

meaning ancient

Domain Archaea contains 2 phyla and domain

Bacteria contains 23 phyla

Determining Relatedness Among

Organisms

The most widely used technique for

determining diversity or relatedness is called

rRNA sequencing

Ribosomes are made up of two subunits: a

small subunit and a large subunit

The small subunit contains only one RNA

molecule - small subunit rRNA or SSU rRNA


Organisms

The SSU rRNA in prokaryotic ribosomes is a 16S

rRNA molecule, whereas the SSU rRNA in

eukaryotes is an 18S rRNA (S refers to

Svedberg unit)Svedberg unit)

The gene that codes for the 16S rRNA molecule

contains about 1500 DNA nucleotides, whereas

the gene that codes for the 18S rRNA molecule

contains about 2000 nucleotides


Organisms

The sequence of nucleotides in the gene that

codes for the 16S rRNA molecule is called the

16S rDNA sequence

In order, to determine relatedness, researchers

compare the sequence of nucleotide base pairs

in the gene rather than comparing the actual

SSU rRNA molecules


Organisms

If the 16S rDNA sequence of one prokaryotic

organism is quite similar to the 16S rDNA

sequence of another prokaryotic organism,

then the organisms are closely relatedthen the organisms are closely related

The less similar the 16S rDNA sequences in

prokaryotes (or the 18S rDNA sequences in

eukaryotes), the less related are the organisms


Organisms

For example, the 18S rDNA sequence of a

human is much more similar to the 18S rDNA

sequence of a chimpanzee than to the 18S sequence of a chimpanzee than to the 18S

rDNA sequence of fungus


Organisms

Perhaps taxonomists will some day combine

the three-domain system and the five-kingdom

system, producing either a six-kingdom system system, producing either a six-kingdom system

(Bacteria, Archaea, Protista, Fungi, Plantae, and

Animalia) or a seven-kingdom system (Bacteria,

Archaea, Algae, Protozoa, Fungi, Plantae, and

Animalia)

Medical Microbiology I - Lecture5

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